Cooper will undergo surgery on his shoulder tomorrow to repair a Grade 3 AC joint injury in his left shoulder after he fell on it awkwardly in a tackle in Queensland's last-minute 30-27 loss to the Melbourne Rebels.

Cooper will use the lengthy recovery window to also undergo arthroscopic surgery to clean up loose cartilage in his hip - a maintenance job that required a break in his playing schedule before it could be fixed.

Cooper's injury leaves Wallabies coach Ewen McKenzie on the hunt for a new No.10 for the upcoming Tests which kick off against France in Brisbane on June 7.

The recovery time for the shoulder operation is 16 weeks, while recovery for the hip surgery will take 12 weeks, meaning it can be slotted in while he is rehabilitating his shoulder. Cooper should be back to full health in mid-September.

Reds head coach Richard Graham reiterated how disappointing the news was for the team and for Cooper.

"Quade is obviously disappointed to miss the rest of the season, but he knows these two operations will bring him back to full health," Graham said.

A standout on the Wallabies' spring tour, Cooper was likely to hold onto his Test starting spot despite the Reds' forgettable Super campaign, but now McKenzie must weigh up the merits of several playmaking contenders.

Brumbies five-eighth Matt Toomua, who made his Test debut in McKenzie's first match in charge of the Wallabies last year, looks the favourite for a recall, but Bernard Foley has soared into contention after a superb season for the Waratahs.

Fellow Waratahs midfielder Kurtley Beale could also slot into the Wallabies playmaking hot seat, a role not unfamiliar to the classy backline utility.

Foley, though, was instrumental again for the Waratahs on Sunday, creating four tries and nailing seven goals from as many attempts to leave Michael Cheika's team in pole position in the race for Australian conference honours.